Zhu Yan, Liu Lihong, Gao Bo, Liu Jing, Qiao Xingchao, Lian Chaojie, He Yongqun
Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China.
National Institutes for Food and Drug Control, Beijing 102627, China.
Evid Based Complement Alternat Med. 2021 Sep 23;2021:6637810. doi: 10.1155/2021/6637810. eCollection 2021.
Traditional Chinese drugs (TCDs) have been widely used in clinical practice in China and many other regions for thousands of years. Nowadays TCD's bioactive ingredients and mechanisms of action are being identified. However, the lack of standardized terminologies or ontologies for the description of TCDs has hindered the interoperability and deep analysis of TCD knowledge and data. By aligning with the Basic Formal Ontology (BFO), an ISO-approved top-level ontology, we constructed a community-driven TCD ontology (TCDO) with the aim of supporting standardized TCD representation and integrated analysis. TCDO provides logical and textual definitions of TCDs, TCD categories, and the properties of TCDs (i.e., nature, flavor, toxicity, and channel tropism). More than 400 popular TCD decoction pieces (TCD-DPs) and Chinese medicinal materials (CMMs) are systematically represented. The logical TCD representation in TCDO supports computer-assisted reasoning and queries using tools such as Description Logic (DL) and SPARQL queries. Our statistical analysis of the knowledge represented in TCDO revealed scientific insights about TCDs. A total of 36 TCDs with medium or high toxicity are most densely distributed, primarily in genus, Lamiids clade, and Fabids clade. TCD toxicity is mostly associated with the hot nature and pungent or bitter flavors and has liver, kidney, and spleen channel tropism. The three pairs of TCD flavor-nature associations (i.e., bitter-cold, pungent-warm, and sweet-neutral) were identified. The significance of these findings is discussed. TCDO has also been used to support the development of a web-based traditional Chinese medicine semantic annotation system that provides comprehensive annotation for individual TCDs. As a novel formal TCD ontology, TCDO lays out a strong foundation for more advanced TCD studies in the future.
数千年来，中药在中国及许多其他地区的临床实践中得到了广泛应用。如今，中药的生物活性成分及作用机制正在逐步明确。然而，缺乏用于描述中药的标准化术语或本体阻碍了中药知识与数据的互操作性及深入分析。通过与国际标准化组织（ISO）批准的顶级本体——基础形式本体（BFO）保持一致，我们构建了一个由社区驱动的中药本体（TCDO），旨在支持中药的标准化表示及综合分析。TCDO提供了中药、中药类别以及中药属性（即性味、毒性和归经）的逻辑和文本定义。系统地表示了400多种常用中药饮片（TCD-DP）和中药材（CMM）。TCDO中的逻辑中药表示支持使用描述逻辑（DL）和SPARQL查询等工具进行计算机辅助推理和查询。我们对TCDO中所表示知识的统计分析揭示了有关中药的科学见解。共有36种中高毒性中药分布最为密集，主要集中在唇形目、豆目分支的属中。中药毒性大多与热性以及辛味或苦味相关，且具有肝、肾、脾经的归经趋向。确定了三对中药性味关联（即苦寒、辛温、甘平）。讨论了这些发现的意义。TCDO还被用于支持基于网络的中药语义注释系统的开发，该系统可为单个中药提供全面注释。作为一种新颖的正式中药本体，TCDO为未来更深入的中药研究奠定了坚实基础。
